Table 3.

Filtered variants in 24 SRNS associated genes

GeneVariantPatients Affected (Heterozygote Unless Hom-Homozygous)dbSNP Ref. No. (Build 135)MAF If Available or ESP Genotype CountHGMDa (Authors’ Comments)PolyPhenMutPred
ACTN4Arg310Gln23rs112545413A=0.0055FSGS (but also in controls)Benign0.459
APOL1Val369Glu20rs143845266ESP: AT-0.003 TT-0.997NoProbably damaging0.831
APOL1Gly247Arg15rs146925617ESP: AG-0.001 GG-0.999NoBenign0.516
APOL1Asn403fs1, 30rs143830837No dataNon/an/a
CD2APPro566Ser2Not in dbSNPESP: TC-0.0002 CC-0.9998NoBenign0.389
COL4A4Ala715Val7rs76636743A=0.0014NoBenign0.282
COL4A4Ala1558Val7Not in dbSNPNo dataNoUnknown0.418
COL4A4Arg877Gln6rs150979437ESP: TC-0.005 CC-0.995NoUnknown0.526
COL4A4Ser969b24 (hom)rs35138315No dataAlport syndromen/an/a
COL4A4Gly999Glu23, 29rs13027659T=0.0073NoUnknown0.6
COL4A4Met1399Leu17rs149117087No dataNoUnknown0.508
COQ2Asn228Ser8rs121918232No dataCoenzyme Q10 deficiencyProbably damaging0.75
COQ2Leu234fs8Not in dbSNPNo dataNon/an/a
INF2Arg877Gln7rs142678449ESP: AA-0.0004 AG-0.0168 GG-0.9828NoUnknown0.447
INF2Glu593Lys28Not in dbSNPNo dataNoUnknown0.502
INF2Ile685Va19, 29Not in dbSNPESP: GA-0.0002 AA-0.9998NoUnknown0.527
INF2Val557Gly19Not in dbSNPESP: GT-0.004 TT-0.996NoUnknown0.512
LAMB2Gly1676Ile33Not in dbSNPNo dataNoBenign0.233
LAMB2Arg575Gln28rs61729152T=0.0087NoBenign0.566
MYH9Lys910Gln23 (hom)Not in dbSNPNo dataFechtner syndrome (but also in control)Possibly damaging0.368
MYH9Ala1072Thr2Not in dbSNPNo dataNoBenign0.357
MYH9Lys1775Glu14rs145139708C=0.002NoBenign0.561
MYH9Arg1936Gln10Not in dbSNPNo dataNoPossibly damaging0.203
MYO1EIle531Met34rs140447165C =0.002NoPossibly damaging0.634
NPHS1His1174Tyr21rs115489112A=0.0018NoPossibly damaging0.431
NPHS1Asn1077Ser1, 4, 5, 7, 8, 9, 15, 26, 30 (21 hom)rs4806213C=0.0836CNS (but also in control)Possibly damaging0.269
NPHS1Arg408Gln16, 26rs33950747T=0.0297CNS (but also in control)Possibly damaging0.892
NPHS1Pro264Arg22, 32, 35, 36rs34982899C=0.0105CNS (in a single patient as a compound het)Benign0.77
NPHS1Ala806Gly2 (hom)Not in dbSNPNo dataNoPossibly damaging0.805
NPHS1Glu117Lys11, 16, 18, 24, 25, 26, 35, 36 (1, 2, 4, 12, 20, 30 hom)rs3814995T=0.3423CNS (but also in control)Possibly damaging0.802
NPHS1Arg586Gly1, 4, 30 (hom)Not in dbSNPNo dataFSGSBenign0.824
NPHS1Ala916Ser6rs138173172ESP: AC 0.006 CC 0.994Reported in 1 patient with minimal changePossibly damaging0.72
NPHS1Thr294Ile9, 10rs113825926A=0.0037Reported in 1 patient with minimal changeBenign0.296
NPHS1Val1084fs3 (hom)Not in dbSNPNo dataCNSn/an/a
NPHS2Pro20Leu17rs74315344A=0.0014Nephrotic syndrome, steroid-resistantn/a0.721
NPHS2Arg229Gln6, 10, 27rs61747728T=0.0178FSGSPossibly damaging0.698
NPHS2Ala284Val23 (hom)Not in dbSNPNo dataNephrotic syndrome, steroid-resistantPossibly damaging0.945
NPHS2Phe344fs6, 10Not in dbSNPNo dataFSGSn/an/a
PLCE1Arg321b5 (hom)Not in dbSNPNo dataFSGSn/an/a
PLCE1Leu57Phe19, 29Not in dbSNPNo dataNoPossibly damaging0.106
PMM2Glu197Ala13rs34258285C=0.0119Congenital disorder of glycosylation 1a (but polymorphism)Benign0.826
PTPROHis362Arg34rs141042273ESP: AA-0.999 AG-0.001NoBenign0.392
SMARCAL1Glu377Gln12rs2066518C=0.0603Schimke immuno-osseous dysplasia (report not clearly pathogenic)Possibly damaging0.492
WT1Ala100Gly1, 4 (hom)Not in dbSNPNo dataNoBenign0.723
  • Variants of note in the exome of 24 genes associated with steroid-resistant nephrotic syndrome (SRNS) sequenced in 36 patients. Includes all variants described in Human Genome Mutation Database (HGMD) professional, all novel variants (not being described in single-nucleotide polymorphisms database [dbSNP] or the 1000 Genomes Project), and all variants with an minor allele frequency (MAF)<1% in the 1000 Genomes Project (http://www.1000genomes.org/node/506; allele frequency) or if not available, Exome Variant Server, National Heart, Lung and Blood Institute Exome Sequencing Project (ESP), Seattle, WA (http://evs.gs.washington.edu/EVS/). Where possible, MutPred and PolyPhen scores are also provided. CNS, congenital nephrotic syndrome; n/a, not available.

  • a Professional release: December of 2011.

  • b Nonsense.